AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00190_mthe_reg_100.orf -o00190_mthe_100.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.5 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 MTH139 269 heterodisulfide reductase HdrD related protein #2 MTH255 269 ribosomal protein L7a #3 MTH256 49 ribosomal protein S28 #4 MTH261 24 translation initiation factor eIF-2, gamma subunit #5 MTH262 24 conserved protein #6 MTH358 300 gluthatione-regulated K+/H+ antiporter #7 MTH384 249 unknown #8 MTH387 24 conserved protein #9 MTH388 35 unknown #10 MTH393 41 NADH dehydrogenase (ubiquinone), subunit 1 related protein #11 MTH481 91 H+-transporting ATPase #12 MTH953 35 ATP synthase, subunit D #13 MTH961 212 unknown #14 MTH1001 285 cation-transporting P-ATPase PacL #15 MTH1246 30 NADH dehydrogenase I, subunit N #16 MTH1251 147 conserved protein #17 MTH1502 189 succinate dehydrogenase, flavoprotein subunit #18 MTH1548 118 NADP-reducing hydrogenase, subunit A #19 MTH1850 105 fumarate reductase Motif number 1 ACAGAGAAGATACTCAGAGCCGCAGGACTGGAATAC 1 151 1 TACACCGCAG 0.684059 -119 AGGACTGGAATACAGAGTCCTTGATGAAGAGTCATG 1 174 1 TACACTTGAG 0.687174 -96 GAGATTCAGATAAGCAGGACAGGAAGC 1 253 1 TAAACAGGAG 0.957651 -17 ATTAAAAAGGGAAGGAATAATGGATGCAGATGAGAG 2 11 0 GAAAATGGAG 0.861802 -259 GATCATCCAGTAAGACGCCCAGGAAAACAAGGATTA 2 88 0 TAACCAGGAA 0.535265 -182 TCTCGGTATATAAAACTTGCTGGATACAGATTTTCA 2 151 0 TAACCTGGAA 0.81073 -119 CAGATTGGTGTAATTACCGATGGATGGTAGAAAAAC 2 241 1 TAAAATGGAG 0.913332 -29 CAGAGCCCCGGAATAAACACCGGATACACGAGGCAG 6 101 1 GAAACCGGAA 0.872111 -200 CAGAATGGGATAATGAACACCGGATACAAAAGCTAA 6 134 1 TAAACCGGAA 0.920153 -167 AACTTTTTTTTACTGATATCTGAAGGGTCCCTCTAC 7 128 0 TACACTGAAG 0.869222 -122 TGGCCTTTTTTACTAATATCTGGAGGTTTCTCTACA 7 166 0 TACACTGGAG 0.980302 -84 CCCCGTAAATAATCCTGAATGAGAACATGGA 9 15 0 TAAACTGAAG 0.918248 -21 GACAAACTGATAAAGATATCCGGAAG 11 76 1 TAAACCGGAG 0.979038 -16 CGTAACTAGGTACCGAGCACTGGATGTGCACATCAG 14 55 1 TACACTGGAG 0.980291 -231 AAATAACGTTGAAGAACAGCTGGACTTATGATGGAT 14 123 1 GAAACTGGAT 0.751822 -163 GAATAACGTTGAAGAACAGCTGGTTGACAGAATCCA 14 219 1 GAAACTGGTG 0.790191 -67 ATTTATTCGATAATGATCACTGGGGGTTCTGT 17 7 0 TAAACTGGGG 0.904151 -183 GTTTAACTGTTAATCAAAGATGGATATATGTTTTTA 18 30 0 TAAAATGGAA 0.722202 -89 TGACTCATATGAAAAACTTCAGAATGAACTGAATTT 19 78 0 GAAACAGAAG 0.641213 -28 *** * ***** * Masking position 2 Map Score: 16.9462 Number of sites scoring better than the average of aligned sites = 444 Number in coding regions = 404 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 2 GCTGTGGTTCGGTCCTTCTGAGGACAGGGTTCCT 1 209 1 GTCCTCTAGA 0.920056 -61 TATATATGATGTTCTCTCAGCGGAGCGAACCATC 6 35 0 GTCTTCACGA 0.962056 -266 ATATCTGAAGGGTCCCTCTACAGAAGATTTAGTA 7 115 0 GTCCTCTCGA 0.992466 -135 AATATCTGGAGGTTTCTCTACAGAAACTTTTTTT 7 154 0 GTTTTCTCGA 0.940622 -96 TGGCTAACTCTCCTGAAAAAGGATGT 12 20 0 GTAATCTCGA 0.879398 -16 TTTCATATAAGTTCCGTCTGCGGATTTTCTCTCA 14 185 0 GTCCTCTCGA 0.992466 -101 CATTTAATAAGTTCATTCTGTGGATTCTGTCAAC 14 241 0 GTCATCTTGA 0.896486 -45 TCACCTGTTAGATTCCTCATTTTA 15 1 0 GTTCTCATTA 0.555071 -30 CCCTTCAAGTGTTTAATCATCGGATCCCCTATTT 16 43 1 GTTATCACGA 0.961349 -105 CTTCAATCAGGATCAGTCGCCTGATTTATTCGAT 17 32 0 GTCATCGCGA 0.945348 -158 ACCGGGTGATGGTTCATCACCTGAGCTTGACTTT 17 110 1 GTTCTCACGA 0.983132 -80 TCTCGGTTATGGTTCATCACCTTAACTATTGACT 17 146 1 GTTCTCACTA 0.890084 -44 * *** *** * ** Masking position 14 Map Score: 12.2011 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 122 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 3 ATAATATCAGTTATGTTCCCTGACTATTAATAG 1 60 0 TTATGTTCTA 0.536919 -210 ACAGAGTCCTTGATGAAGAGTCATGCTGTGGTT 1 185 1 TGATGAAGTA 0.915432 -85 ACTTTATATGTGATGAAGCTTTAATTTCTATTA 2 57 1 TGATGAAGTA 0.915446 -213 ACCCACTTCATGTTAATCCATAACTTGGATTAT 2 203 1 TGTTAATCTA 0.710782 -67 GGATTATATATGATGTTCTCTCAGCGGAGCGAA 6 40 0 TGATGTTCTA 0.9496 -261 AAAACGACTATGAAAATCCTTAAAATTTATTAC 7 85 1 TGAAAATCTA 0.563082 -165 TCCATGAATCTGATGTTCAGTGAAAAAATACAT 11 45 0 TGATGTTCTA 0.950119 -47 ATCATATGGATGTTGATGGGTGAATT 13 4 0 TGTTGATGTA 0.728022 -209 GAATCCCTCCTGATGTTAATTGAGTCATTTTAT 13 88 0 TGATGTTATA 0.600058 -125 CAAGCTCAGGTGATGAACCATCACCCGGTCCTC 17 106 0 TGATGAACTA 0.948305 -84 ATAGTTAAGGTGATGAACCATAACCGAGAATAA 17 142 0 TGATGAACTA 0.970403 -48 TATCCATCTTTGATTAACAGTTAAACAGATCTT 18 40 1 TGATTAACTA 0.75142 -79 TGATTTTAACTGATAATCTTTTAAACAATACAG 19 15 0 TGATAATCTA 0.929059 -91 TAATATGTGTTGATAAACAATTAAAATTCAGTT 19 55 1 TGATAAACTA 0.908608 -51 ******** * * Masking position 13 Map Score: 11.7112 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 121 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 4 CTCAGAGCCGCAGGACTGGAATACAGAGTCC 1 163 1 CAGGCTGGAA 0.889208 -107 TTCAGATAAGCAGGACAGGAAGC 1 257 1 CAGGCAGGAA 0.985774 -13 GCCAATTAAAAAGGGAAGGAATAATGGATGC 2 20 0 AAGGAAGGAA 0.857352 -250 CAATTTAATAAAGGTGATTTA 3 39 1 AAGGGATTTA 0.736101 -11 TCTGCTCAACCGGGCCAGGAACCCCACATTC 6 269 1 CGGGCAGGAA 0.960024 -32 TAGGAACCTCCAGGACATGATGGGGTGGGAA 7 12 0 CAGGCATGAT 0.784153 -238 CTTTTTAAAAAAGGTGAGTTAGACCTAAAAA 7 221 0 AAGGGAGTTA 0.86038 -29 CATCCTTTTTCAGGAGAGTTAGCCA 12 21 1 CAGGGAGTTA 0.931572 -15 AGGAATCTAACAGGTGAGGAATT 15 18 1 CAGGGAGGAA 0.99166 -13 TTCTAATCTGAGGGTGATGTATGGATTTAAG 17 67 0 AGGGGATGTA 0.814096 -123 AAGTCAAGCTCAGGTGATGAACCATCACCCG 17 112 0 CAGGGATGAA 0.981759 -78 GTCAATAGTTAAGGTGATGAACCATAACCGA 17 148 0 AAGGGATGAA 0.960571 -42 **** ****** Masking position 4 Map Score: 11.5379 Number of sites scoring better than the average of aligned sites = 440 Number in coding regions = 416 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 GAATTATCCCGGATCATCCAGTAAGACGCCC 2 104 0 GGACATCCAG 0.978551 -166 CCTCATGAGTGGAACGTCCATGTTAACACCA 6 197 0 GGACGTCCAT 0.939269 -104 TGACTCCATAGGAACCTCCAGGACATGATGG 7 20 0 GGACCTCCAG 0.997165 -230 TTCTGTAGAGGGACCCTTCAGATATCAGTAA 7 124 1 GGACCTTCAG 0.975172 -126 TTTCTGTAGAGAAACCTCCAGATATTAGTAA 7 162 1 GAACCTCCAG 0.987722 -88 TTTAATCATCGGATCCCCTATTTTATTACGA 16 54 1 GGACCCCTAT 0.835721 -94 ACAGAACCCCCAGTGATCATTAT 17 3 1 AGACCCCCAG 0.97852 -187 TCAAAGCCTCCAGGTTAAAGAGT 18 106 0 AAACCTCCAG 0.948456 -13 *** ******* Masking position 3 Map Score: 8.10598 Number of sites scoring better than the average of aligned sites = 397 Number in coding regions = 361 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 6 CCTCGTGTATCCGGTGTTTATTCCGGGGCT 6 104 0 CCGGTGTTTA 0.963012 -197 GCTTTTGTATCCGGTGTTCATTATCCCATT 6 137 0 CCGGTGTTCA 0.987188 -164 GAAAGTTAAAATGGTGTTAACATGGACGTT 6 186 1 ATGGTGTTAA 0.840407 -115 TAGAATCATTCCGGTGTTAATGGTGATGAG 10 22 1 CCGGTGTTAA 0.97983 -20 GATATATGGAATGGTGATAAC 11 2 0 ATGGTGATAA 0.704529 -90 GTCCATGAATCTGATGTTCAGTGAAAAAAT 11 49 0 CTGATGTTCA 0.953745 -43 TGAATCCCTCCTGATGTTAATTGAGTCATT 13 92 0 CTGATGTTAA 0.92857 -121 ATAATATAAACTGATGTGCACATCCAGTGC 14 71 0 CTGATGTGCA 0.811326 -215 AATAGGGGATCCGATGATTAAACACTTGAA 16 46 0 CCGATGATTA 0.834192 -102 ACAGAACCCCCAGTGATCATTATCGAATA 17 10 1 CCAGTGATCA 0.752975 -180 ********** Masking position 5 Map Score: 7.15997 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 212 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 7 ATACGATTTCTCATGAAAATCTGTATCCAG 2 138 1 TCATGAAAAT 0.908915 -132 CTCACCCACTTCATGTTAATCCATAACTTG 2 200 1 TCATGTTAAT 0.897729 -70 AGGCTGAATATTATGACAATCTCCCTCATG 6 221 0 TTATGACAAT 0.827785 -80 ACGAAAACGACTATGAAAATCCTTAAAATT 7 82 1 CTATGAAAAT 0.787142 -168 GTTTATGATAATAGAATCATTC 10 3 1 TTATGATAAT 0.947636 -39 TTGAGTCATTTTATGAAATTTAATTTGAAT 13 72 0 TTATGAAATT 0.705075 -141 GAATCCCTCCTGATGTTAATTGAGTCATTT 13 91 0 TGATGTTAAT 0.713714 -122 ATTCAAAAGTTTATGATATTCAACTAATCC 13 143 0 TTATGATATT 0.802166 -70 GAATAGCTAACCATGTAAATGGGTGCCTTG 14 13 1 CCATGTAAAT 0.642049 -273 ACATGATTATTTATGATAATATAAAGTTTT 16 94 0 TTATGATAAT 0.947636 -54 TCATAAATAATCATGTTAATTATTGGTACT 16 108 1 TCATGTTAAT 0.897729 -40 CTGCCAAACCTTATAATAATGA 17 178 1 TTATAATAAT 0.564934 -12 ********** Masking position 3 Map Score: 7.28604 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 89 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 8 AATAGTTGTCAGCAGCCCTGAGAAAAAGAA 1 35 0 AGCAGCCCTG 0.8801 -235 GAAGATACTCAGAGCCGCAGGACTGGAATA 1 156 1 AGAGCCGCAG 0.95159 -114 TCATCCAGTAAGACGCCCAGGAAAACAAGG 2 92 0 AGACGCCCAG 0.919919 -178 CCATCAGATCAGAGCCCCGGAATAAACACC 6 92 1 AGAGCCCCGG 0.9836 -209 AATGGGATAATGAACACCGGATACAAAAGC 6 137 1 TGAACACCGG 0.830787 -164 AAAGAAGCCCAGAATGTGGGGT 6 289 0 AGAAGCCCAG 0.969152 -12 ATAACGTTGAAGAACAGCTGGACTTATGAT 14 125 1 AGAACAGCTG 0.910773 -161 ATAACGTTGAAGAACAGCTGGTTGACAGAA 14 221 1 AGAACAGCTG 0.910773 -65 GAACGTCCGTAGAGGACCGGGTGATGGTTC 17 95 1 AGAGGACCGG 0.961007 -95 ********** Masking position 8 Map Score: 4.87744 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 237 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 TCTGCCTCTTCAAGGAACCCTGTCCTCAGA 1 225 0 CAAGGAACCC 0.990872 -45 TAATATTCAGCCTGGCACTCATGGTCCTCC 6 238 1 CCTGGCACTC 0.944187 -63 CTCAACCGGGCCAGGAACCCCACATTCTGG 6 273 1 CCAGGAACCC 0.991539 -28 TGAATGAGAACATGGAAGCC 9 1 0 CATGGAAGCC 0.955587 -35 ATCAAGGTGGCAAGGCACCCATTTACATGG 14 23 0 CAAGGCACCC 0.991539 -263 ********** Masking position 7 Map Score: 2.90809 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 87 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 10 TTATCTGAATCTCTGCCTCTTCAAGGAACCCT 1 234 0 CTCTGCCTTC 0.927494 -36 CTCTCATCTGCATCCATTATTCCT 2 3 1 CTCATCCATC 0.990541 -267 TATAAAGGTACTCACCCACTTCATGTTAATCC 2 190 1 CTCACCCTTC 0.96711 -80 CTCATCACCATTAACACCGGAA 10 30 0 CTCATCCATT 0.931425 -12 AATTCACCCATCAACATCCATATGATTG 13 7 1 CCCATCCATC 0.969898 -206 CAATGTTGTTCTCATATCCATCATAAGTCCAG 14 142 0 CTCATACATC 0.931425 -144 TTACGGCAGCCTCTTCCCCTTCAAGTGTTTAA 16 27 1 CTCTTCCTTC 0.97221 -121 ****** **** Masking position 11 Map Score: 3.03738 Number of sites scoring better than the average of aligned sites = 300 Number in coding regions = 287 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 11 ACCCTGTCCTCAGAAGGACCGAACCACAGC 1 209 0 CAGAAGGACC 0.917464 -61 ATACACGAGGCAGAATGGGATAATGAACAC 6 124 1 CAGAATGGGA 0.935182 -177 CCCGGTTGAGCAGAAGGAGGACCATGAGTG 6 253 0 CAGAAGGAGG 0.953395 -48 AAAGAAGCCCAGAATGTGGGGTTCCTGGC 6 282 0 CAGAATGTGG 0.796751 -19 TTACTGATATCTGAAGGGTCCCTCTACAGA 7 125 0 CTGAAGGGTC 0.736925 -125 GTAAATAATCCTGAATGAGAACATGGAAGC 9 12 0 CTGAATGAGA 0.887895 -24 GCTTGGTTAACTGAATGGGATTAGTTGAAT 13 126 1 CTGAATGGGA 0.867249 -87 AGAAAATCCGCAGACGGAACTTATATGAAA 14 189 1 CAGACGGAAC 0.798065 -97 ACAGAATCCACAGAATGAACTTATTAAATG 14 245 1 CAGAATGAAC 0.945921 -41 TGAAAAACTTCAGAATGAACTGAATTTTAA 19 75 0 CAGAATGAAC 0.945921 -31 ********** Masking position 4 Map Score: 3.84528 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 215 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 12 ACAGAGTCCTTGATGAAGAGTCATGCTGTGG 1 185 1 TGATGAAGAT 0.954722 -85 ACTTTATATGTGATGAAGCTTTAATTTCTAT 2 57 1 TGATGAAGCT 0.970723 -213 CAAGCTCAGGTGATGAACCATCACCCGGTCC 17 108 0 TGATGAACCT 0.984481 -82 ATAGTTAAGGTGATGAACCATAACCGAGAAT 17 144 0 TGATGAACCT 0.984481 -46 TATCCATCTTTGATTAACAGTTAAACAGATC 18 40 1 TGATTAACAT 0.88546 -79 TAATATGTGTTGATAAACAATTAAAATTCAG 19 55 1 TGATAAACAT 0.88546 -51 ********* * Masking position 6 Map Score: 3.41762 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 20 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 13 AACATAACTGATATTATGGTTATCTACTTC 1 76 1 ATATTATGGT 0.870015 -194 GCTTCATCACATATAAAGTTTTGCTGCCAA 2 46 0 ATATAAAGTT 0.919224 -224 TACCGAGAACATATAAAGGTACTCACCCAC 2 179 1 ATATAAAGGT 0.947073 -91 TATGGATTATATATGATGTTCTCTCAGCGG 6 46 0 ATATGATGTT 0.781554 -255 ATTTATGATAATATAAAGTTTTCTATATAA 16 86 0 ATATAAAGTT 0.919224 -62 TTATCAACACATATTAAGGTTTGTGATTTT 19 41 0 ATATTAAGGT 0.925812 -65 ********** Masking position 6 Map Score: 1.68044 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 24 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 14 CCCAGGAAAACAAGGATTAATAGAAATTAA 2 77 0 CAAGGATTAA 0.741644 -193 TAATCCAAGTTATGGATTAACATGAAGTGG 2 205 0 TATGGATTAA 0.938031 -65 TTCCTGTTATTATGGATTATATATGATGTT 6 56 0 TATGGATTAT 0.924735 -245 TAATAAATTTTAAGGATTTTCATAGTCGTT 7 87 0 TAAGGATTTT 0.890042 -163 ATGTTCTCATTCAGGATTATTTACGGGG 9 18 1 TCAGGATTAT 0.699702 -18 TCGGCAATCATATGGATGTTGATGGGTGAA 13 13 0 TATGGATGTT 0.699702 -200 ATGTGCTAATTAAAGATTTAAGAC 14 272 1 TAAAGATTTA 0.661694 -14 GAGGGTGATGTATGGATTTAAGCCTTCAAT 17 59 0 TATGGATTTA 0.924733 -131 TCAAATATATTATAGATTAAGGACAAAAGA 18 69 0 TATAGATTAA 0.748785 -50 ********** Masking position 6 Map Score: 1.32046 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 63 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 15 TTCCCCCCATGGGTGTATTCGTGG 1 5 1 CCCCATGGGT 0.87159 -265 TGACAATCTCCCTCATGAGTGGAACGTCCA 6 208 0 CCTCATGAGT 0.872626 -93 GCAGAAGGAGGACCATGAGTGCCAGGCTGA 6 244 0 GACCATGAGT 0.936798 -57 TTCTCATATCCATCATAAGTCCAGCTGTTC 14 136 0 CATCATAAGT 0.821601 -150 GCCGTAATAACCCCATGAGTCCT 16 4 0 CCCCATGAGT 0.935124 -144 ********** Masking position 5 Map Score: 1.2202 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 39 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432